How can I discover gene function on a bacterial genome
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4.3 years ago
vicslab • 0

I have a bacterial genome, but I need more information about it.

I have made Roary to have the clusters of orthologous genes, like OrthoMLC does. I would like to know what softwares I can use to discover the biological function of these genes. I want to split these groups into their functions to have a better understanding.

gene bacteria ontology geneontology • 1.4k views
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You can use eggNOG-mapper

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https://sourceforge.net/projects/fun4me/ This package might help.

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4.3 years ago
h.mon 35k

Prokka is a very fast and efficient bacterial genome annotation pipeline. You can install it with conda and run locally the annotation.

RAST is an annotation server, in addition to a good annotation, it also provides lots of summaries and figures about the annotation. There is a waiting line, but it shouldn't take longer than a day do finish one genome.

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4.3 years ago
onestop_data ▴ 330

Prokka can be complicated to install because of tbl2asn dependency. I show as part of this tutorial on how you can use it step-by-step .

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The fix might be really around the corner, since tbl2asn-forever hack is now on bioconda: https://anaconda.org/bioconda/tbl2asn-forever

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Thanks. I saw the tweet, but I was not aware it was on conda already.

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I have updated the blog post.

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